MPI-CBG ZibAmira Portal

This portal provides an image processing service for academia / research in
cell biology. The purpose is to demonstrate automated tracing of
microtubules from 3D image stacks obtained from electron tomography.

This was developed as part of a research project on the organization of
microtubules in C.elegans embryo ([1]). The service is offered for
non-commercial research purposes only, without warranty that it will
produce the expected result. However, limited support can be obtained by
contacting amitube@mpi-cbg.de and feedback is welcome.
Electron tomograms can be submitted on line using the "Processing Task
Subscription Form" below.

The 3D stacks must be in the MRC format([2]) as
obtained by reconstruction of electron tomograms
using the IMOD software ([3], [4] and
link to imod) for example.

The missing wedge parameters used are assuming that
the data come from dual-tilt
tomography with an angular range close to ±60°. The data needs to be 32-bit
real or byte (8-bits) (MRC mode 0 or 2). The
contrast of 8 bit images needs to be adjusted to fit the 8-bit range as
good as possible. The file size is limited to 10 GB.
The tracing software will use the pixel size from the MRC file. This
information is required. It was tested with pixel sizes up to 4nm.
If you need more detailed explanation of the requirements, please, click
more.

Please fill the form below. The email address is mandatory, it will
be used to send you a link to the result data and to inform you when the
process is completed.

Before sending big files, please note that the time
of file upload is heavily dependent on the file size and available
bandwidth. We cannot guarantee a bandwidth for this system as it depends
on the load of our servers and on end-user internet connection.
The IMOD file will be checked upon arrival for a pixel size between 10 to 50 Angstroms.
If it does not comply, it will not be processed.
Upon job completion, you will receive an e-mail stating the location of the results.
Note, that your data (maximum size: 10 GB) will be deleted 14 days after submission.